de.charite.compbio.jannovar.hgvs.nts.variant

Class NucleotideChangeAllele

java.lang.Object

de.charite.compbio.jannovar.hgvs.nts.variant.NucleotideChangeAllele

All Implemented Interfaces:

ConvertibleToHGVSString, Iterable<NucleotideChange>, Collection<NucleotideChange>, List<NucleotideChange>

public final class NucleotideChangeAllele
extends Object
implements ConvertibleToHGVSString, List<NucleotideChange>

Contains the NucleotideChanges on one allee. Examples:

• [(33A>C);(33A>C)]
• [33A>C;33A>C]
• [33A>C;(33A>C)]

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor and Description
NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes) Construct allele with the given a variant VariantConfiguration and NucleotideChanges.

Method Summary

Modifier and Type	Method and Description
void	add(int index, NucleotideChange element) Deprecated.
boolean	add(NucleotideChange e) Deprecated.
boolean	addAll(Collection<? extends NucleotideChange> c) Deprecated.
boolean	addAll(int index, Collection<? extends NucleotideChange> c) Deprecated.
static NucleotideChangeAllele	build(VariantConfiguration varConfig, NucleotideChange... changes)
void	clear() Deprecated.
boolean	contains(Object o)
boolean	containsAll(Collection<?> c)
boolean	equals(Object obj)
NucleotideChange	get(int index)
com.google.common.collect.ImmutableList<NucleotideChange>	getChanges()
VariantConfiguration	getVarConfig()
int	hashCode()
int	indexOf(Object o)
boolean	isEmpty()
Iterator<NucleotideChange>	iterator()
int	lastIndexOf(Object o)
ListIterator<NucleotideChange>	listIterator()
ListIterator<NucleotideChange>	listIterator(int index)
NucleotideChange	remove(int index) Deprecated.
boolean	remove(Object o) Deprecated.
boolean	removeAll(Collection<?> c) Deprecated.
boolean	retainAll(Collection<?> c) Deprecated.
NucleotideChange	set(int index, NucleotideChange element) Deprecated.
static NucleotideChangeAllele	singleChangeAllele(NucleotideChange change)
int	size()
List<NucleotideChange>	subList(int fromIndex, int toIndex)
Object[]	toArray()
<T> T[]	toArray(T[] a)
String	toHGVSString() Return HGVS representation in three-letter amino acid code.
String	toHGVSString(AminoAcidCode code) Return HGVS representation using the given amino acid code.
String	toString()
NucleotideChangeAllele	withOnlyPredicted(boolean flag)

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.List

replaceAll, sort, spliterator

Methods inherited from interface java.util.Collection

parallelStream, removeIf, stream

Methods inherited from interface java.lang.Iterable

forEach

Constructor Detail

NucleotideChangeAllele

public NucleotideChangeAllele(VariantConfiguration varConfig,
                              Collection<? extends NucleotideChange> changes)

Construct allele with the given a variant VariantConfiguration and NucleotideChanges.

Parameters:

varConfig - configuration of the changes

changes - nucleotide changes to store in the allele

Method Detail

singleChangeAllele

public static NucleotideChangeAllele singleChangeAllele(NucleotideChange change)

Returns:

a new allele containing one nucleotide change

build

public static NucleotideChangeAllele build(VariantConfiguration varConfig,
                                           NucleotideChange... changes)

Returns:

a new allele with the given variant configuration and changes

withOnlyPredicted

public NucleotideChangeAllele withOnlyPredicted(boolean flag)

Returns:

Allele with the onlyPredicted state of all contained changes set to the given value

getVarConfig

public VariantConfiguration getVarConfig()

Returns:

the VariantConfiguration of this allele

getChanges

public com.google.common.collect.ImmutableList<NucleotideChange> getChanges()

Returns:

list of NucleotideChanges

toHGVSString

public String toHGVSString()

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Parameters:

code - AminoAcidCode to use

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Specified by:

hashCode in interface Collection<NucleotideChange>

Specified by:

hashCode in interface List<NucleotideChange>

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Specified by:

equals in interface Collection<NucleotideChange>

Specified by:

equals in interface List<NucleotideChange>

Overrides:

equals in class Object

size

public int size()

Specified by:

size in interface Collection<NucleotideChange>

Specified by:

size in interface List<NucleotideChange>

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface Collection<NucleotideChange>

Specified by:

isEmpty in interface List<NucleotideChange>

contains

public boolean contains(Object o)

Specified by:

contains in interface Collection<NucleotideChange>

Specified by:

contains in interface List<NucleotideChange>

iterator

public Iterator<NucleotideChange> iterator()

Specified by:

iterator in interface Iterable<NucleotideChange>

Specified by:

iterator in interface Collection<NucleotideChange>

Specified by:

iterator in interface List<NucleotideChange>

toArray

public Object[] toArray()

Specified by:

toArray in interface Collection<NucleotideChange>

Specified by:

toArray in interface List<NucleotideChange>

toArray

public <T> T[] toArray(T[] a)

Specified by:

toArray in interface Collection<NucleotideChange>

Specified by:

toArray in interface List<NucleotideChange>

add

@Deprecated
public boolean add(NucleotideChange e)

Deprecated.

Specified by:

add in interface Collection<NucleotideChange>

Specified by:

add in interface List<NucleotideChange>

remove

@Deprecated
public boolean remove(Object o)

Deprecated.

Specified by:

remove in interface Collection<NucleotideChange>

Specified by:

remove in interface List<NucleotideChange>

containsAll

public boolean containsAll(Collection<?> c)

Specified by:

containsAll in interface Collection<NucleotideChange>

Specified by:

containsAll in interface List<NucleotideChange>

addAll

@Deprecated
public boolean addAll(Collection<? extends NucleotideChange> c)

Deprecated.

Specified by:

addAll in interface Collection<NucleotideChange>

Specified by:

addAll in interface List<NucleotideChange>

addAll

@Deprecated
public boolean addAll(int index,
                                  Collection<? extends NucleotideChange> c)

Deprecated.

Specified by:

addAll in interface List<NucleotideChange>

removeAll

@Deprecated
public boolean removeAll(Collection<?> c)

Deprecated.

Specified by:

removeAll in interface Collection<NucleotideChange>

Specified by:

removeAll in interface List<NucleotideChange>

retainAll

@Deprecated
public boolean retainAll(Collection<?> c)

Deprecated.

Specified by:

retainAll in interface Collection<NucleotideChange>

Specified by:

retainAll in interface List<NucleotideChange>

clear

@Deprecated
public void clear()

Deprecated.

Specified by:

clear in interface Collection<NucleotideChange>

Specified by:

clear in interface List<NucleotideChange>

get

public NucleotideChange get(int index)

Specified by:

get in interface List<NucleotideChange>

set

@Deprecated
public NucleotideChange set(int index,
                                        NucleotideChange element)

Deprecated.

Specified by:

set in interface List<NucleotideChange>

add

@Deprecated
public void add(int index,
                            NucleotideChange element)

Deprecated.

Specified by:

add in interface List<NucleotideChange>

remove

@Deprecated
public NucleotideChange remove(int index)

Deprecated.

Specified by:

remove in interface List<NucleotideChange>

indexOf

public int indexOf(Object o)

Specified by:

indexOf in interface List<NucleotideChange>

lastIndexOf

public int lastIndexOf(Object o)

Specified by:

lastIndexOf in interface List<NucleotideChange>

listIterator

public ListIterator<NucleotideChange> listIterator()

Specified by:

listIterator in interface List<NucleotideChange>

listIterator

public ListIterator<NucleotideChange> listIterator(int index)

Specified by:

listIterator in interface List<NucleotideChange>

subList

public List<NucleotideChange> subList(int fromIndex,
                                      int toIndex)

Specified by:

subList in interface List<NucleotideChange>